9KLM | pdb_00009klm

Cryo-EM structure of the monomeric Rhodobacter sphaeroides G1C LH1-RC core complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

From Genome to structure: Elucidating Neurosporene Production in the Rhodobacter sphaeroides G1C Mutant

Wu, Y.-L.Yu, L.-J.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainA [auth L]282Cereibacter sphaeroidesMutation(s): 0 
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides)
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UniProt GroupP0C0Y8
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainB [auth M]308Cereibacter sphaeroidesMutation(s): 0 
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides)
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UniProt GroupP0C0Y9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein H chainC [auth H]260Cereibacter sphaeroidesMutation(s): 0 
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides)
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UniProt GroupP0C0Y7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B-875 alpha chain54Cereibacter sphaeroidesMutation(s): 0 
UniProt
Find proteins for P0C0X9 (Cereibacter sphaeroides)
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UniProt GroupP0C0X9
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna pigment protein beta chain49Cereibacter sphaeroidesMutation(s): 0 
UniProt
Find proteins for Q7B300 (Cereibacter sphaeroides)
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UniProt GroupQ7B300
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
protein-UFA [auth U]53Cereibacter sphaeroidesMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Intrinsic membrane protein PufXGA [auth X]82Cereibacter sphaeroidesMutation(s): 0 
UniProt
Find proteins for Q7B2Z6 (Cereibacter sphaeroides)
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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FB [auth M],
IB [auth M],
NC [auth E],
VC [auth F]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL (Subject of Investigation/LOI)
Query on BCL

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AC [auth C]
DC [auth c]
DD [auth G]
DE [auth n]
FD [auth g]
AC [auth C],
DC [auth c],
DD [auth G],
DE [auth n],
FD [auth g],
FE [auth O],
HA [auth L],
HC [auth D],
ID [auth I],
IE [auth o],
KE [auth P],
MC [auth d],
MD [auth i],
ME [auth p],
NE [auth Q],
OA [auth L],
OB [auth A],
OD [auth J],
PC [auth E],
PE [auth q],
QB [auth a],
SB [auth B],
TC [auth e],
TD [auth j],
VD [auth K],
WA [auth M],
WC [auth F],
XB [auth b],
YD [auth k],
ZA [auth M],
ZC [auth f],
ZD [auth N]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)
Query on BPH

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AB [auth M],
IA [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10 (Subject of Investigation/LOI)
Query on U10

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CB [auth M],
JA [auth L],
KA [auth L]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PGV (Subject of Investigation/LOI)
Query on PGV

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CD [auth G]
HB [auth M]
LA [auth L]
LB [auth H]
MA [auth L]
CD [auth G],
HB [auth M],
LA [auth L],
LB [auth H],
MA [auth L],
MB [auth H],
QC [auth E],
TA [auth L],
UA [auth L],
WD [auth K],
XA [auth M],
YB [auth C],
ZB [auth C]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
A1EF2 (Subject of Investigation/LOI)
Query on A1EF2

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AE [auth N]
BC [auth C]
BE [auth N]
CE [auth n]
ED [auth g]
AE [auth N],
BC [auth C],
BE [auth N],
CE [auth n],
ED [auth g],
FC [auth c],
GB [auth M],
GD [auth g],
GE [auth O],
HE [auth o],
JC [auth D],
KC [auth D],
LC [auth d],
LD [auth I],
LE [auth p],
ND [auth J],
OE [auth q],
PD [auth J],
QD [auth J],
RB [auth a],
RC [auth E],
SC [auth e],
SD [auth J],
UB [auth B],
WB [auth b],
XD [auth k],
YC [auth f]
(6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},26~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-2,6,8,10,12,14,16,18,20,22,26,30-dodecaene
C40 H58
ATCICVFRSJQYDV-XILUKMICSA-N
LMT (Subject of Investigation/LOI)
Query on LMT

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AD [auth G]
BD [auth G]
CC [auth c]
DB [auth M]
EB [auth M]
AD [auth G],
BD [auth G],
CC [auth c],
DB [auth M],
EB [auth M],
EC [auth c],
EE [auth O],
GC [auth D],
HD [auth I],
IC [auth D],
JB [auth H],
JD [auth I],
JE [auth P],
KB [auth H],
NB [auth A],
OC [auth E],
PB [auth a],
QE [auth U],
RA [auth L],
SA [auth L],
TB [auth B],
TE [auth X],
UC [auth F],
VA [auth L],
VB [auth b]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
LDA (Subject of Investigation/LOI)
Query on LDA

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KD [auth I]
NA [auth L]
PA [auth L]
QA [auth L]
RD [auth J]
KD [auth I],
NA [auth L],
PA [auth L],
QA [auth L],
RD [auth J],
RE [auth X],
SE [auth X],
UD [auth K],
XC [auth F],
YA [auth M]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
BB [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A [auth L]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2022YFC3401800

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release